Re: [apbs-users] apolar solvation energy calculation

Hello -
You can remove the volume term by setting the press variable to zero and can remove the LJ integral term by setting bconc to zero.
Thanks,
--
Nathan Baker
Laboratory Fellow
Pacific Northwest National Laboratory
+1-509-375-3997
http://www.linkedin.com/in/nathanandrewbaker/
From: Rosana Collepardo [mailto:r.collepardo@...]
Sent: Wednesday, October 30, 2013 2:43 AM
To: apbs-users@...
Subject: [apbs-users] apolar solvation energy calculation
Hello,
I am trying to calculate an approximate apolar solvation energy of a protein with apbs and wanted to know if the parameter files for LJ radii and well-depths are already available?
Alternatively, is it possible to use a simpler approach that does not require these parameters? For instance: surften*SASA as discussed in the iAPBS paper?
Many thanks!
Rosana

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Hello,
I am trying to calculate an approximate apolar solvation energy of a
protein with apbs and wanted to know if the parameter files for LJ radii
and well-depths are already available?
Alternatively, is it possible to use a simpler approach that does not
require these parameters? For instance: surften*SASA as discussed in the
iAPBS paper?
Many thanks!
Rosana

Hello -
You can remove the volume term by setting the press variable to zero and can remove the LJ integral term by setting bconc to zero.
Thanks,
--
Nathan Baker
Laboratory Fellow
Pacific Northwest National Laboratory
+1-509-375-3997
http://www.linkedin.com/in/nathanandrewbaker/
From: Rosana Collepardo [mailto:r.collepardo@...]
Sent: Wednesday, October 30, 2013 2:43 AM
To: apbs-users@...
Subject: [apbs-users] apolar solvation energy calculation
Hello,
I am trying to calculate an approximate apolar solvation energy of a protein with apbs and wanted to know if the parameter files for LJ radii and well-depths are already available?
Alternatively, is it possible to use a simpler approach that does not require these parameters? For instance: surften*SASA as discussed in the iAPBS paper?
Many thanks!
Rosana